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Corante Blogs examine, through the eyes of leading observers, analysts, thinkers, and doers, critical themes and memes in technology, business, law, science, and culture.

The Press Will Be Outsourced Before Stopped

Vin Crosbie, on the challenges, financial and otherwise, that newspaper publishers are facing: "The real problem, Mr. Newspaperman, isn't that your content isn't online or isn't online with multimedia. It's your content. Specifically, it's what you report, which stories you publish, and how you publish them to people, who, by the way, have very different individual interests. The problem is the content you're giving them, stupid; not the platform its on."
by Vin Crosbie in Rebuilding Media

Travels In Numerica Deserta

There's a problem in the drug industry that people have recognized for some years, but we're not that much closer to dealing with it than we were then. We keep coming up with these technologies and techniques which seem as if they might be able to help us with some of our nastiest problems - I'm talking about genomics in all its guises, and metabolic profiling, and naturally the various high-throughput screening platforms, and others. But whether these are helping or not (and opinions sure do vary), one thing that they all have in common is that they generate enormous heaps of data.
by Derek Lowe in In the Pipeline

Disrobing the Emperor: The online “user experience” isn't much of one

Now that the Web labor market is saturated and Web design a static profession, it's not surprising that 'user experience' designers and researchers who've spent their careers online are looking for new worlds to conquer. Some are returning to the “old media” as directors and producers. More are now doing offline consulting (service experience design, social policy design, exhibition design, and so on) under the 'user experience' aegis. They argue that the lessons they've learned on the Web can be applied to phenomena in the physical and social worlds. But there are enormous differences...
by Bob Jacobson in Total Experience

Second Life: What are the real numbers?

Clay Shirky, in deconstructing Second Life hype: "Second Life is heading towards two million users. Except it isn’t, really... I suspect Second Life is largely a 'Try Me' virus, where reports of a strange and wonderful new thing draw the masses to log in and try it, but whose ability to retain anything but a fraction of those users is limited. The pattern of a Try Me virus is a rapid spread of first time users, most of whom drop out quickly, with most of the dropouts becoming immune to later use."
by Clay Shirky in Many-to-Many

The democratisation of everything

Over the last few years we've seen old barriers to creativity coming down, one after the other. New technologies and services makes it trivial to publish text, whether by blog or by print-on-demand. Digital photography has democratised a previously expensive hobby. And we're seeing the barriers to movie-making crumble, with affordable high-quality cameras and video hosting provided by YouTube or Google Video and their ilk... Music making has long been easy for anyone to engage in, but technology has made high-quality recording possible without specialised equipment, and the internet has revolutionised distribution, drastically disintermediating the music industry... What's left? Software maybe? Or maybe not."
by Suw Charman in Strange Attractor

RNA Interference: Film at Eleven

Derek Lowe on the news that the Nobel Prize for medicine has gone to Craig Mello and Andrew Fire for their breakthrough work: "RNA interference is probably going to have a long climb before it starts curing many diseases, because many of those problems are even tougher than usual in its case. That doesn't take away from the discovery, though, any more than the complications of off-target effects take away from it when you talk about RNAi's research uses in cell culture. The fact that RNA interference is trickier than it first looked, in vivo or in vitro, is only to be expected. What breakthrough isn't?"
by Derek Lowe in In the Pipeline

PVP and the Honorable Enemy

Andrew Phelps: "Recently my WoW guild has been having a bit of a debate on the merits of Player-vs.-Player (PvP) within Azeroth. My personal opinion on this is that PvP has its merits, and can be incredible fun, but the system within WoW is horridly, horribly broken. It takes into account the concept of the battle, but battle without consequence, without emotive context, and most importantly, without honor..."

From later in the piece: "When I talk about this with people (thus far anyway) I typically get one of two responses, either 'yeah, right on!' or 'hey, it’s war, and war isn’t honorable – grow the hell up'. There is a lot to be said for that argument – but the problem is that war in the real historical world has very different constraints that are utterly absent from fantasized worlds..."
by Andrew Phelps in Got Game

Rats Rule, Right?

Derek Lowe: "So, you're developing a drug candidate. You've settled on what looks like a good compound - it has the activity you want in your mouse model of the disease, it's not too hard to make, and it's not toxic. Everything looks fine. Except. . .one slight problem. Although the compound has good blood levels in the mouse and in the dog, in rats it's terrible. For some reason, it just doesn't get up there. Probably some foul metabolic pathway peculiar to rats (whose innards are adapted, after all, for dealing with every kind of garbage that comes along). So, is this a problem?.."
by Derek Lowe in In the Pipeline

Really BAD customer experience at Albertsons Market

Bob Jacobson, on shopping at his local Albertsons supermarket where he had "one of the worst customer experiences" of his life: "Say what you will about the Safeway chain or the Birkenstock billionaires who charge through the roof for Whole Foods' organic fare, they know how to create shopping environments that create a more pleasurable experience, at its best (as at Whole Foods) quite enjoyable. Even the warehouses like Costco and its smaller counterpart, Smart & Final, do just fine: they have no pretentions, but neither do they dump virtual garbage on the consumer merely to create another trivial revenue stream, all for the sake of promotions in the marketing department..."
by Strange Attractor in Total Experience

The Guardian's "Comment is Free"

Kevin Anderson: "First off, I want to say that I really admire the ambition of the Guardian Unlimited’s Comment is Free. It is one of the boldest statements made by any media company that participation needs to be central to a radical revamp of traditional content strategies... It is, therfore, not hugely surprising to find that Comment is Free is having a few teething troubles..."
by Kevin Anderson in strange
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

The Loom

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January 06, 2005

From Enemies to Friends

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Posted by Carl Zimmer

bacteriophage2.gifWhen you consider a tapeworm or an Ebola virus, it is easy think of them as being evil to their very core. That's a mistake. It's true that at this point in their evolutionary history these species have become well adapted to living inside of other organisms (us), and using our resources to help them reproduce themselves even if we get sick in the process. But one of the big lessons of modern biology is that there are no essences in nature--only the ongoing interplay of natural selection and the conditions in which it works. If the conditions change, organisms may evolve into drastically different things. Even the most ruthless parasite may discover the virtues of peace and harmony--if the conditions are right.

Joel Sachs and James Bull, two biologists at the University of Texas, have offered a vivid demonstration of this fact with the help of bacteria-infecting viruses, called bacteriophages. Bacteriophages, such as the one shown here, are wickedly elegant in the way they find hosts and inject their DNA, which then hijacks the bacteria's cellular machinery to make new bacteriophages. (For more of my praise of the bacteriophage, plus an excellent movie of the beast, go here.)

Bacteriophages fit the definition of parasite to a T. In many cases new viruses multiply inside a host until the bacterium simply rips apart. In other cases, they make bacteria sick, draining resources from their hosts that could otherwise be used for the hosts' own reproduction. But, as Bull and his colleagues have shown in a series of experiments, bacteriophages are not malicious in their very essence. Depending on the conditions in which bacteriophages find themselves, they can evolve into milder forms, or into meaner ones.

Bull and his colleagues took advantage of the fact that many bacteriophages can infect new hosts in one of two ways--by escaping one bacterium to invade another, or by getting passed down from one bacterium to its offspring. These two routes are called horizontal and vertical transmission. Bull's team experimentally created conditions that favored vertical transmission, and within a few dozen generations the viruses became much milder. If you rely on your host's survival for your own survival, it doesn't pay to be a brutal killer. (I wrote more about this evolutionary trade-off--and some of the debate surrounding it--in this article for Science.)

Now Bull and Sachs show that bacteriophages can even evolve to be nice to other bacteriophages. They describe the experiment in the January 11 issue of the Proceedings of the National Academy of Sciences. They started out with two bacteriophages, called f1 and IKe. Both viruses infect E. coli bacteria, but they enter in different ways. f1 only grabs onto one type of hair on the surface of E. coli (the F pilus), while IKe invades its hosts through another type (the N pilus). In the wild, f1 and IKe don't get along well. If they end up in the same host, they compete for the bacterium's cellular machinery. Also, because they are close relatives, sharing the same 10 genes, DNA-binding proteins of one bacteriophage can accidentally grab the DNA of the other species. As a result, bacteria infected with both f1 and IKe produce fewer copies of each virus than bacteria infected with only one species. It's the classic Darwinian scramble.

But Bull and Sachs wondered what would happen if the survival of both bacteriophages actually depended on their coexistence. Here's how they answered the question. First they engineered both bacteriophages, adding a gene that provides resistance to a different antibiotic (kanamycin for IKe and chloramphenicol for f1). Then they dumped billions of the engineered viruses into beakers full of E. coli. They allowed the viruses 16 minutes to find hosts, invade them, and start producing the proteins that confer antibiotic resistance. Then they added the two antibiotics to the beakers. Only the bacteria that had been infected with both bacteriophages could survive the assault. If a bacterium harbored only f1, for example, it would still die, because it remained susceptible to kanamycin.

Next, Bull and Sachs let the bacteriophages and their hosts alone for an hour. The bacteria divided, while the bacteriophages made copies of themselves. After an hour, the scientists dissolved away the bacteria, leaving behind the viruses. These new viruses were then added to a fresh batch of bacteria, and the cycle repeated itself.

Viruses are notoriously sloppy at replicating. The odds of a new virus winding up with a mutation is much higher than for organisms like ourselves, equipped as we are with enzymes that act like genetic proofreaders. As a result, with each round of Bull and Sachs' experiment, many variants emerged in both the f1 and IKe populations. The variants that were best suited for reproducing in the experimental conditions were favored by natural selection, and over time the viruses evolved. After 50 rounds, Bull and Sachs stopped the experiment and took a look at what the bacteriophages had become. Were they so selfish that they had driven themselves extinct? Or had they come to some sort of accommodation?

The bacteriophages clearly went through natural selection during just 50 rounds. By that point f1 was producing 50 times more copies of itself, and IKe was producing 1,000 times more. At the beginning of the experiment sharing a host was a bad thing for these viruses, but at the end it had become a very good thing. Bull and Sachs discovered that they had overcome their conflict of interest in an extraordinary way: they practically merged into a single organism. When Bull and Sachs opened up a bacteriophage shell, very often they found both the f1 and IKe genomes sitting side by side. They cold still find plenty of viruses with a single genome inside, but even in these cases, evolution had taken a dramatic turn. By about round 20, the IKe viruses had lost the ability to make their own protein coat. Instead, they borrowed f1 coats.

Bull and Sachs argue that the bacteriophages adapted to the experiment in a clever way. If you're a bacteriophage, successfully invading a host on your own is not enough to stave off death, because you may find yourself alone. If a mutation lets you bring along the other virus with you, then you are pretty much guaranteed survival. For some reason, f1 seems to have taken the lead in this cooperation, mutating in such a way that IKe genomes could slip easily inside f1's protein coats. As a result, IKe began to lose its own ability to survive as an independent virus, relying instead on the cooperation of f1. Once the viruses were packaged together, they no longer had a conflict of interest, and they could evolve an even greater level of cooperation.

Evolutionary biologists have long been fascinated by cooperation, whether the cooperators are chromosomes in a single cell, individual bacteria in a colony, or people in a village. What keeps individuals from cheating on others, from choosing the selfish strategy rather than the selfless one? Scientists have constructed sophisticated mathematical models in order to find the right sort of conditions where cooperation might evolve. But Bull and Sachs point out that it only took them 50 generations to turn uncooperative bacteriophages into intimate partners. When they sequenced the viruses, they found that f1 had acquired just eight mutations in its DNA, and IKe had acquired nine. Perhaps cooperation is not such a big deal after all. And perhaps parasites are not the essence of evil we tend to believe them to be.

Comments (8) + TrackBacks (0) | Category: Evolution


COMMENTS

1. Aaron on January 6, 2005 04:51 PM writes...

A fantastic, fascinating post!!!!!!!

p.s. "They cold still find plenty of viruses..."? Because I'm sure you don't have to deal with enough persnickety editors already. ;)

Permalink to Comment

2. John S Bolton on January 7, 2005 05:44 AM writes...

That leads on to optimistic thoughts, yet the conditions forcing cooperation in the experiment are so stringent, that they resemble males and females of the same species.

Permalink to Comment

3. p on January 9, 2005 08:27 PM writes...

Very interesting findings!

Some question I have:
What really seperates the two entities as bacteriophages?

Do the new entities really consititute f1 and IKe or are they already something else, something new?

I guess where I am going is that the changes induced are signficant and speak to th epower of mutation and selection to drive categorical changes.

Permalink to Comment

4. David Govett on January 12, 2005 06:04 PM writes...

Why anthropomorphize virii, especially since there is question as to whether or not they live? Also, mitochondria once were extracytal bacteria, so should they now be considered malevolent symbiotes?

Permalink to Comment

5. David Govett on January 12, 2005 07:02 PM writes...

Re: "...within a few dozen generations the viruses became much milder. If you rely on your host's survival for your own survival, it doesn't pay to be a brutal killer."
Might not this explain the residence of mitochondria within our cells?

Permalink to Comment

6. Piers Young on January 13, 2005 11:33 AM writes...

I'm probably being slow, but why does the 50-generation benchmark mean that co-operation isn't such a big thing? I'd have thought that the speed of the "love match" served to highlight the importance of the co-operation?

Permalink to Comment

7. p on January 13, 2005 09:58 PM writes...

David, Interesting point.

Permalink to Comment

8. Pastor Bentonit on January 15, 2005 12:38 AM writes...

Well, how cool is that. I worked on those two phage strains (species?) a few years ago (physical studies on virion stability). Intrested parties may here note that both f1 and IKe are indeed "mild" parasites, persistently infecting E. coli, so that the bacterium does not lyse (burst) on the release of newly assembled phage. Instead, these are continuously set free at the cell surface as the bacteria divide (at a slightly lower rate than non-infected cells).

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